Shotgun optical maps of the whole Escherichia coli 0157:H7 genome

Alex Lim; Eileen T. Dimalanta; Konstantinos D. Potamousis; Galex Yen; Jennifer Apodoca; Chunhong Tao; Jieyi Lin; Rong Qi; John Skiadas; Arvind Ramanathan; Nicole T. Perna; Guy Plunkett; Valerie Burland; Bob Mau; Jeremiah Hackett; Frederick R. Blattner; Thomas S. Anantharaman; Bhubaneswar Mishra; David C. Schwartz

doi:10.1101/gr.172101

Shotgun optical maps of the whole Escherichia coli 0157:H7 genome

Alex Lim, Eileen T. Dimalanta, Konstantinos D. Potamousis, Galex Yen, Jennifer Apodoca, Chunhong Tao, Jieyi Lin, Rong Qi, John Skiadas, Arvind Ramanathan, Nicole T. Perna, Guy Plunkett, Valerie Burland, Bob Mau, Jeremiah Hackett, Frederick R. Blattner, Thomas S. Anantharaman, Bhubaneswar Mishra, David C. Schwartz

Research output: Contribution to journal › Article › peer-review

74 Scopus citations

Abstract

We have constructed Nhel and Xhol optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.

Original language	English (US)
Pages (from-to)	1584-1593
Number of pages	10
Journal	Genome Research
Volume	11
Issue number	9
DOIs	https://doi.org/10.1101/gr.172101
State	Published - 2001

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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Lim, A., Dimalanta, E. T., Potamousis, K. D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., Perna, N. T., Plunkett, G., Burland, V., Mau, B., Hackett, J., Blattner, F. R., Anantharaman, T. S., Mishra, B., & Schwartz, D. C. (2001). Shotgun optical maps of the whole Escherichia coli 0157:H7 genome. Genome Research, 11(9), 1584-1593. https://doi.org/10.1101/gr.172101

Lim, A, Dimalanta, ET, Potamousis, KD, Yen, G, Apodoca, J, Tao, C, Lin, J, Qi, R, Skiadas, J, Ramanathan, A, Perna, NT, Plunkett, G, Burland, V, Mau, B, Hackett, J, Blattner, FR, Anantharaman, TS, Mishra, B & Schwartz, DC 2001, 'Shotgun optical maps of the whole Escherichia coli 0157:H7 genome', Genome Research, vol. 11, no. 9, pp. 1584-1593. https://doi.org/10.1101/gr.172101

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abstract = "We have constructed Nhel and Xhol optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.",

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AU - Apodoca, Jennifer

AU - Tao, Chunhong

AU - Lin, Jieyi

AU - Qi, Rong

AU - Skiadas, John

AU - Ramanathan, Arvind

AU - Perna, Nicole T.

AU - Plunkett, Guy

AU - Burland, Valerie

AU - Mau, Bob

AU - Hackett, Jeremiah

AU - Blattner, Frederick R.

AU - Anantharaman, Thomas S.

AU - Mishra, Bhubaneswar

AU - Schwartz, David C.

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AB - We have constructed Nhel and Xhol optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.

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Shotgun optical maps of the whole Escherichia coli 0157:H7 genome

Abstract

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